Multi-environment genomic selection in rice elite breeding lines

Nguyen Van Hieu, Morantte Rose Imee Zhella, Lopena Vitaliano, Verdeprado Holden, Murori Rosemary, Ndayiragije Alexis, Kumar Katiyar Sanjay, Islam Md Rafiqul, Juma Roselyne Uside, Flandez-Galvez Hayde, Glaszmann Jean-Christophe, Cobb Joshua N., Bartholome Jérôme. 2023. Multi-environment genomic selection in rice elite breeding lines. Rice, 16 (1)

Résumé : Background: Assessing the performance of elite lines in target environments is essential for breeding programs to select the most relevant genotypes. One of the main complexities in this task resides in accounting for the genotype by environment interactions. Genomic prediction models that integrate information from multi-environment trials and environmental covariates can be efficient tools in this context. The objective of this study was to assess the predictive ability of different genomic prediction models to optimize the use of multi-environment information. We used 111 elite breeding lines representing the diversity of the international rice research institute breeding program for irrigated ecosystems. The lines were evaluated for three traits (days to flowering, plant height, and grain yield) in 15 environments in Asia and Africa and genotyped with 882 SNP markers. We evaluated the efficiency of genomic prediction to predict untested environments using seven multi-environment models and three cross-validation scenarios. Results: The elite lines were found to belong to the indica group and more specifically the indica-1B subgroup which gathered improved material originating from the Green Revolution. Phenotypic correlations between environments were high for days to flowering and plant height (33% and 54% of pairwise correlation greater than 0.5) but low for grain yield (lower than 0.2 in most cases). Clustering analyses based on environmental covariates separated Asia's and Africa's environments into different clusters or subclusters. The predictive abilities ranged from 0.06 to 0.79 for days to flowering, 0.25–0.88 for plant height, and − 0.29–0.62 for grain yield. We found that models integrating genotype-by-environment interaction effects did not perform significantly better than models integrating only main effects (genotypes and environment or environmental covariates). The different cross-validation scenarios showed that, in most cases, the use of all available environments gave better results than a subset. Conclusion: Multi-environment genomic prediction models with main effects were sufficient for accurate phenotypic prediction of elite lines in targeted environments. These results will help refine the testing strategy to update the genomic prediction models to improve predictive ability.

Mots-clés Agrovoc : Oryza sativa, génotype, phénotype, amélioration des plantes, amélioration génétique, sélection, riz, génome, génomique, modélisation environnementale, méthode statistique, Oryza, caractère agronomique

Mots-clés géographiques Agrovoc : Afrique, Philippines

Mots-clés libres : Riz, Sélection génomique, Essais multilocaux

Classification Agris : F30 - Génétique et amélioration des plantes

Champ stratégique Cirad : CTS 2 (2019-) - Transitions agroécologiques

Agences de financement hors UE : Bill and Melinda Gates Foundation, Agropolis Fondation

Auteurs et affiliations

• Nguyen Van Hieu, CIRAD-BIOS-UMR AGAP (FRA)
• Morantte Rose Imee Zhella, IRRI [International Rice Research Institute] (PHL)
• Lopena Vitaliano, IRRI [International Rice Research Institute] (PHL)
• Verdeprado Holden, IRRI [International Rice Research Institute] (PHL)
• Murori Rosemary, IRRI [International Rice Research Institute] (PHL)
• Ndayiragije Alexis, IRRI [International Rice Research Institute] (MOZ)
• Kumar Katiyar Sanjay, IRRI [International Rice Research Institute] (PHL)
• Islam Md Rafiqul, IRRI [International Rice Research Institute] (PHL)
• Juma Roselyne Uside, IRRI [International Rice Research Institute] (PHL)
• Flandez-Galvez Hayde, University of the Philippines (PHL)
• Glaszmann Jean-Christophe, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-9918-875X
• Cobb Joshua N., IRRI [International Rice Research Institute] (PHL)
• Bartholome Jérôme, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-0855-3828 - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/608208/)

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